Join objects which using the same material
Fear not my friend. Here I come with help for You :) You have to open text editor in Blender, click New to create new text file, and paste this code snippet (below), then change "somename" to the materials name before .001 (f.ex. if it's Material, Material.001 and so on, You have to write Material there). Then press Run Script and watch the magic (it should select all objects having material with this name part).Important is to keep indentations cause Python is very sensitive about it, so in line 1 and 2 there is no indentation line 3 - 4 spaces, line 5 - 8 spaces, line 6 - 12 spaces.

import bpy
scene = bpy.context.scene
for ob in scene.objects:
    for slot in ob.material_slots:
        if ("somename" in slot.name):
            ob.select = True